Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013930.1 Corchorus olitorius cultivar O-4 contig13963, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26588
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:1039 original size:10 final size:10
Alignment explanation
Indices: 1026--1066 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
1016 AATATGTTTT
1026 TATATCTTAC
1 TATATCTTAC
1036 TATATCTTAC
1 TATATCTTAC
1046 --TATCTTATC
1 TATATCTTA-C
1055 T-TATCTTAC
1 TATATCTTAC
1064 TAT
1 TAT
1067 CTTACTACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
8 7 0.25
9 3 0.11
10 18 0.64
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.54
Consensus pattern (10 bp):
TATATCTTAC
Found at i:1051 original size:8 final size:8
Alignment explanation
Indices: 1028--1073 Score: 56
Period size: 8 Copynumber: 5.2 Consensus size: 8
1018 TATGTTTTTA
1028 TATCTTAC
1 TATCTTAC
1036 TATATCTTAC
1 --TATCTTAC
1046 TATCTTATC
1 TATCTTA-C
1055 TTATCTTAC
1 -TATCTTAC
1064 TATCTTAC
1 TATCTTAC
1072 TA
1 TA
1074 CTATATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
8 17 0.50
9 2 0.06
10 15 0.44
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (8 bp):
TATCTTAC
Found at i:1051 original size:18 final size:18
Alignment explanation
Indices: 1028--1073 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
1018 TATGTTTTTA
1028 TATCTTACTATATCTTAC
1 TATCTTACTATATCTTAC
1046 TATCTTATCT-TATCTTAC
1 TATCTTA-CTATATCTTAC
1064 TATCTTACTA
1 TATCTTACTA
1074 CTATATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.08
18 22 0.85
19 2 0.08
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (18 bp):
TATCTTACTATATCTTAC
Found at i:2128 original size:1 final size:1
Alignment explanation
Indices: 2122--2211 Score: 63
Period size: 1 Copynumber: 90.0 Consensus size: 1
2112 TAGCTTTCGT
* * * * * * * * *
2122 AAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAAACAAAAACAAAAACAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * *
2187 AACAAAAACAAAAACAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
2212 GTACGTAAAT
Statistics
Matches: 63, Mismatches: 26, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 63 1.00
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2135 original size:7 final size:7
Alignment explanation
Indices: 2123--2211 Score: 136
Period size: 7 Copynumber: 13.6 Consensus size: 7
2113 AGCTTTCGTA
2123 AAAAAAC
1 AAAAAAC
2130 AAAAAAC
1 AAAAAAC
2137 AAAAAAC
1 AAAAAAC
2144 AAAAAAC
1 AAAAAAC
2151 AAAAAAC
1 AAAAAAC
2158 AAAAAAC
1 AAAAAAC
2165 AAAAAAC
1 AAAAAAC
2172 -AAAAAC
1 AAAAAAC
2178 -AAAAAC
1 AAAAAAC
2184 -AAAAAC
1 AAAAAAC
2190 -AAAAAC
1 AAAAAAC
2196 -AAAAAC
1 AAAAAAC
2202 -AAAAAC
1 AAAAAAC
2208 AAAA
1 AAAA
2212 GTACGTAAAT
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
6 36 0.44
7 45 0.56
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:3030 original size:22 final size:22
Alignment explanation
Indices: 3005--3109 Score: 95
Period size: 22 Copynumber: 4.8 Consensus size: 22
2995 CATAGAAAGA
* **
3005 TTATCAAAATTTTGTAGTGTGG
1 TTATCAAAACTTCATAGTGTGG
*
3027 TTATCAAAACTTCATA-TAGAGG
1 TTATCAAAACTTCATAGT-GTGG
*
3049 TTATCAAAACTTCATAGTGTAG
1 TTATCAAAACTTCATAGTGTGG
* ** *
3071 TTATCAAAATTTCATACAGAGG
1 TTATCAAAACTTCATAGTGTGG
* *
3093 TTACCAAAATTTCATAG
1 TTATCAAAACTTCATAG
3110 GGATGGAGGT
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.01
22 66 0.97
23 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (22 bp):
TTATCAAAACTTCATAGTGTGG
Found at i:3053 original size:44 final size:44
Alignment explanation
Indices: 3005--3109 Score: 147
Period size: 44 Copynumber: 2.4 Consensus size: 44
2995 CATAGAAAGA
** * *
3005 TTATCAAAATTTTGTAGTGTGGTTATCAAAACTTCATATAGAGG
1 TTATCAAAATTTCATAGTGTAGTTATCAAAACTTCATACAGAGG
* *
3049 TTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATACAGAGG
1 TTATCAAAATTTCATAGTGTAGTTATCAAAACTTCATACAGAGG
*
3093 TTACCAAAATTTCATAG
1 TTATCAAAATTTCATAG
3110 GGATGGAGGT
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (44 bp):
TTATCAAAATTTCATAGTGTAGTTATCAAAACTTCATACAGAGG
Found at i:3178 original size:22 final size:22
Alignment explanation
Indices: 3139--3203 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
3129 TTGTGCTTAT
** *
3139 CAAAATTTCCTAGAGAGGTTAA
1 CAAAATTTTATAGGGAGGTTAA
*
3161 CAAAATTTTATAGGGAGGTTAT
1 CAAAATTTTATAGGGAGGTTAA
*
3183 GAAAATTTTAT-GGAGAGGTTA
1 CAAAATTTTATAGG-GAGGTTA
3204 TCGAAAATAC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.05
22 35 0.95
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.32
Consensus pattern (22 bp):
CAAAATTTTATAGGGAGGTTAA
Found at i:3204 original size:22 final size:23
Alignment explanation
Indices: 3151--3211 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
3141 AAATTTCCTA
**
3151 GAGAGGTTAACAAAATTTTATAG
1 GAGAGGTTATGAAAATTTTATAG
3174 G-GAGGTTATGAAAATTTTAT-G
1 GAGAGGTTATGAAAATTTTATAG
3195 GAGAGGTTATCGAAAAT
1 GAGAGGTTAT-GAAAAT
3212 ACATAGAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 2 0.06
22 25 0.74
23 7 0.21
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.31
Consensus pattern (23 bp):
GAGAGGTTATGAAAATTTTATAG
Found at i:3217 original size:108 final size:108
Alignment explanation
Indices: 3022--3217 Score: 234
Period size: 108 Copynumber: 1.8 Consensus size: 108
3012 AATTTTGTAG
* * * *
3022 TGTGGTTATCAAAACTTCATATAGAGGTTATCAAAACTTCATAGTGTAGTTATCAAAATTTCATA
1 TGTGCTTATCAAAACTTCATAGAGAGGTTAACAAAACTTCATAGTGGAGTTATCAAAATTTCATA
*
3087 CAGAGGTTACCAAAATTTCATAGGGATGGAGGTTACCAAAATT
66 CAGAGGTTACCAAAATTACATAGGGATGGAGGTTACCAAAATT
* * * * * *
3130 TGTGCTTATCAAAATTTCCTAGAGAGGTTAACAAAATTTTATAG-GGAGGTTATGAAAATTTTAT
1 TGTGCTTATCAAAACTTCATAGAGAGGTTAACAAAACTTCATAGTGGA-GTTATCAAAATTTCAT
** *
3194 GGAGAGGTTATCGAAAA-TACATAG
65 ACAGAGGTTA-CCAAAATTACATAG
3218 AGAGGATATC
Statistics
Matches: 72, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
107 2 0.03
108 65 0.90
109 5 0.07
ACGTcount: A:0.37, C:0.11, G:0.19, T:0.33
Consensus pattern (108 bp):
TGTGCTTATCAAAACTTCATAGAGAGGTTAACAAAACTTCATAGTGGAGTTATCAAAATTTCATA
CAGAGGTTACCAAAATTACATAGGGATGGAGGTTACCAAAATT
Found at i:3274 original size:22 final size:23
Alignment explanation
Indices: 3249--3482 Score: 80
Period size: 22 Copynumber: 10.6 Consensus size: 23
3239 CTCATAAAGA
* * *
3249 GGTTATCGAAA-TTTCATGGTGT
1 GGTTATCAAAATTTTCATAGTGC
3271 GGTTATCAAAATTTTCATAGTGC
1 GGTTATCAAAATTTTCATAGTGC
* *
3294 GGTTA-C-CAATTTT-ATTTAGTGT
1 GGTTATCAAAATTTTCA--TAGTGC
* *
3316 GATTATTAAAATTTT-ATAG-GC
1 GGTTATCAAAATTTTCATAGTGC
* * * *
3337 AGATTATCAAAA-TTTCACACTGA
1 -GGTTATCAAAATTTTCATAGTGC
* * *
3360 GATTATCGAAA-TTTCATAGTGT
1 GGTTATCAAAATTTTCATAGTGC
* * * *
3382 GGTTACCCAAA-TTTCACAGTGT
1 GGTTATCAAAATTTTCATAGTGC
* * * *
3404 GGTTATC-GAATTTTGATAGGGA
1 GGTTATCAAAATTTTCATAGTGC
* **
3426 GGTTATCGAAA-TTTCATA-TTA
1 GGTTATCAAAATTTTCATAGTGC
* * * *
3447 GGTTATC-AAATTTGCAAAATGT
1 GGTTATCAAAATTTTCATAGTGC
*
3469 GGTTATCAATATTT
1 GGTTATCAAAATTT
3483 CTACATTGTA
Statistics
Matches: 163, Mismatches: 36, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
20 4 0.02
21 25 0.15
22 105 0.64
23 22 0.13
24 7 0.04
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (23 bp):
GGTTATCAAAATTTTCATAGTGC
Found at i:3372 original size:44 final size:43
Alignment explanation
Indices: 3324--3441 Score: 112
Period size: 44 Copynumber: 2.7 Consensus size: 43
3314 GTGATTATTA
*
3324 AAATTTTATAGGCAGATTATCAAAATTTCACACTGAGATTATCG
1 AAATTTTATAGG-AGGTTATCAAAATTTCACACTGAGATTATCG
* * * * * * *
3368 AAATTTCATAGTGTGGTTACCCAAATTTCACAGTGTGGTTATCG
1 AAATTTTATAG-GAGGTTATCAAAATTTCACACTGAGATTATCG
*
3412 -AATTTTGATAGGGAGGTTATCGAAATTTCA
1 AAATTTT-ATA-GGAGGTTATCAAAATTTCA
3442 TATTAGGTTA
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
43 5 0.08
44 52 0.88
45 2 0.03
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.36
Consensus pattern (43 bp):
AAATTTTATAGGAGGTTATCAAAATTTCACACTGAGATTATCG
Found at i:3410 original size:66 final size:65
Alignment explanation
Indices: 3340--3483 Score: 148
Period size: 66 Copynumber: 2.2 Consensus size: 65
3330 TATAGGCAGA
* * *
3340 TTATCAAAATTTCACACTGAGATTATCGAAATTTCATAGTGT-GGTTACCCAAATTT-CACAGTG
1 TTATCAAAATTTCACACGGAGATTATCGAAATTTCATA-T-TAGGTTA-CCAAATTTGCAAAATG
3403 TGG
63 TGG
* * * * * * *
3406 TTATCGAATTTTGATAGGGAGGTTATCGAAATTTCATATTAGGTTATCAAATTTGCAAAATGTGG
1 TTATCAAAATTTCACACGGAGATTATCGAAATTTCATATTAGGTTACCAAATTTGCAAAATGTGG
*
3471 TTATCAATATTTC
1 TTATCAAAATTTC
3484 TACATTGTAG
Statistics
Matches: 62, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
64 8 0.13
65 23 0.37
66 31 0.50
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.38
Consensus pattern (65 bp):
TTATCAAAATTTCACACGGAGATTATCGAAATTTCATATTAGGTTACCAAATTTGCAAAATGTGG
Found at i:5252 original size:22 final size:22
Alignment explanation
Indices: 5211--5795 Score: 227
Period size: 22 Copynumber: 26.4 Consensus size: 22
5201 ACAATCAAAC
* *
5211 CAAAATTACATAGTAAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5233 TAAAATTTCATAGTGTGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
5255 CAAAATTTCATA-TGGAGGTTAT
1 CAAAATTTCATAGT-GAGGTTAT
* * *
5277 CAAAACTTCGTAGTGTA-ATTAT
1 CAAAATTTCATAGTG-AGGTTAT
** *
5299 CAAAATTTCATACAGAGGTTAC
1 CAAAATTTCATAGTGAGGTTAT
*
5321 CAAAATTTCATA-TAAAAAGGTTAT
1 CAAAATTTCATAGT---GAGGTTAT
* *
5345 CAAAATTTCTTA-TGGAGATTAT
1 CAAAATTTCATAGT-GAGGTTAT
*
5367 CAAAATTTCATACG-AAGGTTAT
1 CAAAATTTCATA-GTGAGGTTAT
** * * *
5389 TGAAATTTTATAGTGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
* * * *
5411 -AAAAATTAATTAG-AACGTTAT
1 CAAAATTTCA-TAGTGAGGTTAT
**
5432 CAAAA-TT--T-GT--TCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
5448 CAAAATTTCTTAG-GATGGTTAA
1 CAAAATTTCATAGTGA-GGTTAT
* *
5470 CAAAATTTCATAGGGAGCTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5492 GAAAATATT-ATGGAGAGGTTAT
1 CAAAAT-TTCATAGTGAGGTTAT
**
5514 CAAAATTAT-ATA-TAGAGAATAT
1 CAAAATT-TCATAGT-GAGGTTAT
* * *
5536 CACAATTTCATTCTTATAGGGAAGTTAT
1 CA-AA----ATT-TCATAGTGAGGTTAT
* * *
5564 CGAAATTTCATGGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
5586 CAAAATTTTCATAGTGCGATTA-
1 CAAAA-TTTCATAGTGAGGTTAT
* * * * *
5608 C-CAATTTTATAATGTGATTAT
1 CAAAATTTCATAGTGAGGTTAT
5629 CAAAATTTCATAGACAATGAGGTTAT
1 CAAAATTTCATAG----TGAGGTTAT
* * *
5655 CAAAACTTCATTGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5677 CAGAATTTCACAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5699 CAAAATTTCACATTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* *
5721 CAAATTTTCATAGGGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* * *
5743 CGAAATTTCACAATGAGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
* ** *
5765 CAAATTTTCGCAGTGTGGTTAT
1 CAAAATTTCATAGTGAGGTTAT
*
5787 CAATATTTC
1 CAAAATTTC
5796 TACATTGGAG
Statistics
Matches: 418, Mismatches: 107, Indels: 76
0.70 0.18 0.13
Matches are distributed among these distances:
16 9 0.02
17 3 0.01
18 1 0.00
19 1 0.00
20 14 0.03
21 19 0.05
22 296 0.71
23 24 0.06
24 18 0.04
26 18 0.04
27 6 0.01
28 9 0.02
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (22 bp):
CAAAATTTCATAGTGAGGTTAT
Found at i:5396 original size:68 final size:68
Alignment explanation
Indices: 5229--5387 Score: 191
Period size: 68 Copynumber: 2.4 Consensus size: 68
5219 CATAGTAAGG
* ** * **
5229 TTATTAAAATTTCATAGTGTGGTTACCAAAATTTCATAT--GGAGGTTATCAAAACTTCGTAGTG
1 TTATCAAAATTTCATACAGAGGTTACCAAAATTTCATATAAAAAGGTTATCAAAACTTCGTAGTG
*
5292 TAA
66 GAA
* *
5295 TTATCAAAATTTCATACAGAGGTTACCAAAATTTCATATAAAAAGGTTATCAAAATTTCTTA-TG
1 TTATCAAAATTTCATACAGAGGTTACCAAAATTTCATATAAAAAGGTTATCAAAACTTCGTAGTG
5359 GAGA
66 GA-A
5363 TTATCAAAATTTCATAC-GAAGGTTA
1 TTATCAAAATTTCATACAG-AGGTTA
5388 TTGAAATTTT
Statistics
Matches: 80, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
66 35 0.44
67 4 0.05
68 41 0.51
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (68 bp):
TTATCAAAATTTCATACAGAGGTTACCAAAATTTCATATAAAAAGGTTATCAAAACTTCGTAGTG
GAA
Found at i:10618 original size:21 final size:20
Alignment explanation
Indices: 10594--10651 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
10584 TGAAGCCCTT
10594 GAGGAAGCAAGAAAGAAAGCA
1 GAGGAAGCAAGAAAGAAAG-A
*
10615 GAGGAAG-AAGAGAAGGAAAGG
1 GAGGAAGCAAGA-AA-GAAAGA
*
10636 GAGAAAGCAGAGAAAG
1 GAGGAAGCA-AGAAAG
10652 CGGAGAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
20 4 0.13
21 16 0.52
22 8 0.26
23 3 0.10
ACGTcount: A:0.55, C:0.05, G:0.40, T:0.00
Consensus pattern (20 bp):
GAGGAAGCAAGAAAGAAAGA
Found at i:14711 original size:10 final size:11
Alignment explanation
Indices: 14684--14709 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
14674 ATTGAAAATT
14684 AATTTATTAAA
1 AATTTATTAAA
14695 AATTTATTAAA
1 AATTTATTAAA
14706 AATT
1 AATT
14710 ATAATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (11 bp):
AATTTATTAAA
Found at i:19183 original size:29 final size:28
Alignment explanation
Indices: 19147--19206 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 28
19137 ATAGATTAAT
* *
19147 ACAACAACACTACAATTACAAGTTTTCA
1 ACAACAACACCACAATTACAAGCTTTCA
19175 ACAATCAACACCACAATTACAAGCTTTCA
1 ACAA-CAACACCACAATTACAAGCTTTCA
19204 ACA
1 ACA
19207 CTAACTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.47, C:0.28, G:0.03, T:0.22
Consensus pattern (28 bp):
ACAACAACACCACAATTACAAGCTTTCA
Found at i:19266 original size:14 final size:14
Alignment explanation
Indices: 19247--19295 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
19237 TCCATCATCC
19247 AAATAAAATTCATG
1 AAATAAAATTCATG
* *
19261 AAATAATTATT-ATCC
1 AAATAA-AATTCAT-G
19276 AAATAAAATTCATG
1 AAATAAAATTCATG
19290 AAATAA
1 AAATAA
19296 TTAACATCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (14 bp):
AAATAAAATTCATG
Found at i:19275 original size:29 final size:29
Alignment explanation
Indices: 19243--19298 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
19233 CAAATCCATC
19243 ATCCAAATAAAATTCATGAAATAATTATT
1 ATCCAAATAAAATTCATGAAATAATTATT
19272 ATCCAAATAAAATTCATGAAATAATTA
1 ATCCAAATAAAATTCATGAAATAATTA
19299 ACATCTTGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.32
Consensus pattern (29 bp):
ATCCAAATAAAATTCATGAAATAATTATT
Found at i:19366 original size:22 final size:22
Alignment explanation
Indices: 19319--19366 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
19309 CTTCTTAGTG
*
19319 TATATATAATTATAAATCAATC
1 TATATATAATTATAAACCAATC
19341 TATATATAATTATAAACCCAAT-
1 TATATATAATTATAAA-CCAATC
19363 TATA
1 TATA
19367 AAGCCCAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (22 bp):
TATATATAATTATAAACCAATC
Found at i:20136 original size:17 final size:17
Alignment explanation
Indices: 20116--20149 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20106 ATTTTATGGA
20116 TATTTAT-ATTATTAATT
1 TATTTATAATT-TTAATT
20133 TATTTATAATTTTAATT
1 TATTTATAATTTTAATT
20150 GATATGTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTTATAATTTTAATT
Done.